Mercurial > repos > iuc > snpeff

diff snpeff_get_chr_names.xml @ 33:94653948fdb9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5
author iuc
date Sat, 04 Oct 2025 17:00:46 +0000
parents ebe9fd7e5bd1
children
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--- a/snpeff_get_chr_names.xml	Mon Nov 18 22:15:18 2024 +0000
+++ b/snpeff_get_chr_names.xml	Sat Oct 04 17:00:46 2025 +0000
@@ -42,15 +42,15 @@
                 <param name="genomeVersion" type="select" label="Genome">
                     <help>This can only be used on built-in databases manually configured by your galaxy admin.</help>
                     <options from_data_table="snpeffv_genomedb">
-                            <filter type="static_value" name="SNPEFF_VERSION" value="@SNPEFF_VERSION@" column="1"/>
-                            <filter type="unique_value" column="2" />
+                        <filter type="regexp" column="1" value="@COMPATIBLE_DB_VERSIONS_REGEX@" />
+                        <filter type="unique_value" column="2" />
                     </options>
                 </param>
             </when>
             <when value="history">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                     <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help>
-                    <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
+                    <validator type="expression" message="This version of SnpEff will only work with @COMPATIBLE_DB_VERSIONS_STRING@ genome databases">value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@</validator>
                 </param>
             </when>
             <when value="named">
@@ -62,7 +62,7 @@
             <when value="custom">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                     <help>This can only be used on databases in your history that were created using the snpEff build tool.</help>
-                    <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
+                    <validator type="expression" message="This version of SnpEff will only work with @COMPATIBLE_DB_VERSIONS_STRING@ genome databases">value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@</validator>
                 </param>
             </when>
         </conditional>
@@ -72,18 +72,22 @@
     </outputs>
     <tests>
         <test>
-            <param name="genomeSrc" value="named"/>
-            <param name="genome_version" value="Bacillus_subtilis_subsp_subtilis_str_168"/>
+            <conditional name="snpDb">
+                <param name="genomeSrc" value="cached"/>
+                <param name="genomeVersion" value="ebola_zaire"/>
+            </conditional>
             <output name="chr_names">
                 <assert_contents>
-                    <has_text text="Chromosome" />
-                    <has_text text="4215606" />
+                    <has_text text="KJ660346" />
+                    <has_text text="18959" />
                 </assert_contents>
             </output>
         </test>
         <test expect_failure="True">
-            <param name="genomeSrc" value="named"/>
-            <param name="genome_version" value="should_not_match"/>
+            <conditional name="snpDb">
+                <param name="genomeSrc" value="named"/>
+                <param name="genome_version" value="should_not_match"/>
+            </conditional>
         </test>
     </tests>
     <help><![CDATA[